Organiser Samantha Thorpe said a little pond nearby became "like a raging river".

"It has never happened like this before."

Just as amazingly, Ms Thorpe said, within an hour of the deluge, the water had drained away and the sun was shining, as if it hadn't happened.

A general severe thunderstorm warning remains in place for most of the state.

Thunderstorms lashing parts of Victoria have seen up to 13mm of rain fall every five minutes in the early hours of Saturday and a severe weather warning is also in place for parts of Victoria including Shepparton, Seymour, Castlemaine, Kyneton, Ballarat and Wangaratta.

Emergency Management Commissioner Andrew Crisp said the bad weather had been widespread.

"There weren't too many parts of the state that have been spared the impact of the weather event we've seen over the past 48 hours," he said on Saturday.

Bureau of Meteorology's Kevin Parkyn said intense storms and heavy rain were expected to continue in Melbourne on Saturday afternoon and night.

He said the relatively rare weather conditions could bring flash flooding too.

In the 24 hours from 7am on Friday the SES received 693 requests for assistance across the state, with 123 of those calls from the Malvern area.